AAGAB p.Ala3=
c.9T>C · rs180799838 · VCV1599538
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 7.97%, amr) — too common for a highly-penetrant pathogenic allele
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -9.9 | GERP -3 |
| Overall | ||
| CADD | 4.684 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
7.97%
Admixed American · 4,608/57,842 alleles
Filtering AF
7.77%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 7.7%
Overall
0.47%
7,521/1,600,386 alleles · common
exomes 6,200/1,448,064 · genomes 1,321/152,322 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 7.97% | 13 |
| East Asian | 2.13% | 47 |
| Remaining individualsnot grpmax-eligible | 0.511% | 196 |
| Ashkenazi Jewishnot grpmax-eligible | 0.296% | 338 |
| African / African-American | 0.158% | 634 |
| Finnishnot grpmax-eligible | 0.129% | 773 |
| Middle Eastern | 0.124% | 803 |
| European (non-Finnish) | 0.113% | 886 |
| South Asian | 0.0391% | 2,556 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- AAGAB
- Protein
- p.Ala3=
- Coding
- c.9T>C
- MANE Select
- NM_024666
- dbSNP
- rs180799838
- Type
- single nucleotide variant
- Location
- chr15:67254623 (GRCh38)
- Gene constraint
- LOEUF 1.156 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 80.41 · 3 PDB
Similar variants
- AAGAB p.Arg124Ter Pathogenic ★★ same type
- AAGAB p.Arg161Ter Pathogenic ★★ same type
- AAGAB p.Gln21Ter Pathogenic ★★ same type
- AAGAB p.Ala74Pro Uncertain significance ★★ ⚠ same type
- AAGAB p.Arg161Gln Uncertain significance ★★ ⚠ same type
- AAGAB p.Leu92Val Uncertain significance ★★ ⚠ same type
- AAGAB c.264+33A>G Benign ★★ same type
- AAGAB c.536-95G>A Benign ★★ same type
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/aagab-p-ala3 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown